Low Level functionality for getting patches per image level¶
Shows how to call two functions for finding patch locations using
package module code imported from .toolkit
OpenSlide Whole Slide Image file with multiple image levels.
Aperio data from link found here: openslide.org
patch_location_array = get_patch_location_array_for_image_level(run_parameters)¶
# help(get_patch_location_array_for_image_level)
""" Usage:
patch_location_array = get_patch_location_array_for_image_level(run_parameters)
using patch_select_method, find all upper left corner locations of patches
that won't exceed image size givin the 'patch_height' and 'patch_width
Args (run_parameters): python dict.keys()
wsi_filename: file name (with valid path)
patch_height: patch size = (patch_width, patch_height)
patch_width: patch size = (patch_width, patch_height)
thumbnail_divisor: wsi_image full size divisor to create thumbnail image
patch_select_method: 'threshold_rgb2lab' or 'threshold_otsu'
threshold: minimimum sum of thresholded image (default = 0)
image_level: openslide image pyramid level 0,1,2,...
Returns:
patch_location_array: [[x, y], [x, y],... ] n_pairs x 2 numpy array
"""
mask_im, prev_im, patch_array = get_patch_locations_preview_image_for_image_level(run_parameters)¶
# help(get_patch_locations_preview_image_for_image_level)
""" Usage: with run_parameter dict "run_pars"
mask_image, thumb_preview, patch_location_array = get_patch_locations_preview_image_for_image_level(run_pars)
create viewable images to show patch locations
Args (run_parameters): python dict.keys()
wsi_filename: file name (with valid path)
patch_height: patch size = (patch_width, patch_height)
patch_width: patch size = (patch_width, patch_height)
thumbnail_divisor: wsi_image full size divisor to create thumbnail image
patch_select_method: 'threshold_rgb2lab' or 'threshold_otsu'
threshold: sum of thresholded image minimimum (default = 0)
image_level: openslide image pyramid level 0,1,2,...
Optional keys()
border_color: patch-box representation color red, blue, green, ...
Returns:
mask_image: black & white image of the mask
thumb_preview: thumbnail image with patch locations marked
patch_location_array: list of patch locations used [(row, col), (row, col),... ]
"""
First cell imports some extras for notebook display¶
In [3]:
import time
note_book_cell_seq_run_time = time.time()
import os
import sys
from pychunklbl.toolkit import get_patch_location_array_for_image_level
from pychunklbl.toolkit import get_patch_locations_preview_image_for_image_level
from pychunklbl.toolkit import get_file_size_ordered_dict, lineprint_level_sizes_dict, get_level_sizes_dict
DEFAULT_THUMBNAIL_DIVISOR = 20
data_dir = '../../../ncsa/DigiPath_MLTK_data/Aperio'
fs_od = get_file_size_ordered_dict( data_dir, file_type_list=['.svs', '.tif', '.tiff'] )
list_number = 0
for file_name, file_size in fs_od.items():
print('%3i %30s: %i'%(list_number, file_name, file_size) )
list_number += 1
Next cell defines the dictionary of parameters needed to call these two functions¶
In [4]:
""" Select a filename from the list of files available in your data directory
"""
image_file_name = 'CMU-2.svs'
# image_file_name = 'JP2K-33003-2.svs'
# image_file_name = 'CMU-1-Small-Region.svs'
run_parameters = dict()
run_parameters['wsi_filename'] = os.path.join(data_dir, image_file_name)
print('Image File:\n', run_parameters['wsi_filename'])
run_parameters['thumbnail_divisor'] = DEFAULT_THUMBNAIL_DIVISOR
run_parameters['patch_select_method'] = 'threshold_otsu' # 'threshold_rgb2lab'
run_parameters['patch_height'] = 224
run_parameters['patch_width'] = 224
run_parameters['threshold'] = 0
run_parameters['border_color'] = 'blue'
lineprint_level_sizes_dict(run_parameters['wsi_filename'])
In [5]:
level_sizes_dict = get_level_sizes_dict(run_parameters['wsi_filename'])
n_levels = level_sizes_dict['level_count']
for im_lvl in range(0, n_levels):
run_parameters['image_level'] = im_lvl
run_parameters['thumbnail_divisor'] = DEFAULT_THUMBNAIL_DIVISOR
t1 = time.time()
patch_location_array = get_patch_location_array_for_image_level(run_parameters)
print('\nimage_level = %i,\nnumber of patches = %i'%(im_lvl, len(patch_location_array)))
thmb_div_4_level = run_parameters['thumbnail_divisor'] // (2*run_parameters['image_level'] + 1)
run_parameters['thumbnail_divisor'] = thmb_div_4_level
mask_im, prev_im, patch_array = get_patch_locations_preview_image_for_image_level(run_parameters)
print('image_level = %i,\nnumber of patches = %i'%(im_lvl, len(patch_array)))
print('cell run time: %0.3f'%(time.time() - t1))
print('thumb image size:', prev_im.size, 'thumbnail_divisor', run_parameters['thumbnail_divisor'])
display(prev_im)
